github.com/PRIMED-Ancestry-Inference/PCA_projection/LD_pruning

PCA_projection

Project genotypes into PCA space using pre-made SNP loadings.

create_pca_projection

This workflow is used to create a pca projection from a genetic reference dataset (in VCF format). First, the reference data is subsetted to include only sites in common with a provided reference variant file (intended to contain only variants that one would expect to find in all downstream datsets that will be projected using loadings created in this worflow (e.g., a list of common sites t


This is a companion discussion topic for the original entry at github.com/PRIMED-Ancestry-Inference/PCA_projection/LD_pruning